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Opened 6 years ago
Closed 6 years ago
#3104 closed defect (fixed)
Adjusting cage-builder edge length: 'NoneType' object has no attribute 'create_marke
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Higher-Order Structure | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-14) Description Fiddled around with cage builder a bit. Then tried to change the Edge length to a float (1.42, was trying to create a graphene lattice) and got a python error. Then tried inputting the default value 50 and got the same error (the one in the log, don't know if that's exactly the same error as before, but suspect yes). Log: UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/epkumpu/Documents/Models/Split_NanoLuc/4mls.pdb format PDB 4mls.pdb title: Crystal structure of the spytag and spycatcher-DELTAN1 complex [more info...] Chain information for 4mls.pdb #1 --- Chain | Description A | fibronectin binding protein B | spytag > set bgColor white > lighting full > graphics silhouettes true > lighting full > hide cartoons > hide atoms > show surfaces > view > view > mlp Map values for surface "4mls.pdb_A SES surface": minimum -28.01, mean -5.627, maximum 25.77 Map values for surface "4mls.pdb_B SES surface": minimum -19.72, mean -1.978, maximum 19.35 > hide #1.1 models > show #1.1 models > hide #1.2 models > hide #1.1 models > show #1.2 models > open2 > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/model1.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/model2.pdb Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.672 -3.955 0.009 -0.125 -0.031 -2.029 -6.804 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.80401 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.666 -3.876 0.008 -0.131 -0.004 -1.942 -6.610 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.60981 Ignored bad PDB record found on line 14 model1.pdb title: Protein t= 0.00000 [more info...] Chain information for model1.pdb #2 --- Chain | Description | No description available model2.pdb title: Protein t= 0.00000 [more info...] Chain information for model2.pdb #3 --- Chain | Description | No description available > view > hide #!1 models > hide #1.2 models > hide #2 models > show #2 models > hide #3 models > hide #2 models > show #2 models > show #3 models Drag select of 126 atoms, 128 bonds > hide sel atoms > show sel cartoons > view sel > hide sel cartoons > show sel surfaces Drag select of model1.pdb_ SES surface, 287 of 11678 triangles, model2.pdb_ SES surface, 185 of 11762 triangles > select clear > toolshed show Toolbar > hbonds #!2-3 10 hydrogen bonds found > ~hbonds > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker model2.pdb, chain (blank) (#3) with model1.pdb, chain (blank) (#2), sequence alignment score = 23.3 RMSD between 8 pruned atom pairs is 0.229 angstroms; (across all 8 pairs: 0.229) > hide #!2 models > show #!2 models > lighting full > color #!2-3 bychain > color #!2-3 byhetero > mlp #!2-3 Map values for surface "model1.pdb_ SES surface": minimum -23.48, mean -3.399, maximum 20.05 Map values for surface "model2.pdb_ SES surface": minimum -24.47, mean -3.346, maximum 20.57 > tile #2-3 > tile #2-3 columns 2 > tile #2-3 > undo > undo > undo > tile #2-3 columns 2 Expected a keyword > toolshed show "Side View" > set Current settings: Background color: 100,100,100 Subdivision: 1 Expected a keyword Expected a keyword > undo > hide #!2-3 surfaces > graphics silhouettes false > show #!2-3 cartoons > select #2 63 atoms, 64 bonds, 1 model selected > select #3 63 atoms, 64 bonds, 1 model selected > select #2 63 atoms, 64 bonds, 1 model selected > select #3 63 atoms, 64 bonds, 1 model selected > select #2 63 atoms, 64 bonds, 1 model selected > select #3 63 atoms, 64 bonds, 1 model selected > select #2 63 atoms, 64 bonds, 1 model selected Drag select of 16 residues > hide sel cartoons > show sel cartoons > select clear > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > close #3 > mlp #!2 Map values for surface "model1.pdb_ SES surface": minimum -23.48, mean -3.399, maximum 20.05 > graphics silhouettes true > save /Users/epkumpu/Desktop/image12.png supersample 3 > turn y 90 > turn y 90 > turn y 90 > save /Users/epkumpu/Desktop/image13.png supersample 3 > hide #!2 models > open 3v03 Summary of feedback from opening 3v03 fetched from pdb --- notes | Fetching compressed mmCIF 3v03 from http://files.rcsb.org/download/3v03.cif Fetching CCD ACT from http://ligand-expo.rcsb.org/reports/A/ACT/ACT.cif 3v03 title: Crystal structure of Bovine Serum Albumin [more info...] Chain information for 3v03 #3 --- Chain | Description A B | Serum albumin Non-standard residues in 3v03 #3 --- ACT — acetate ion CA — calcium ion 3v03 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select #3 8810 atoms, 8978 bonds, 36 pseudobonds, 3 models selected > view sel > hide sel cartoons > hide sel atoms > show sel surfaces > mlp sel Map values for surface "3v03_A SES surface": minimum -30.45, mean -4.403, maximum 24.02 Map values for surface "3v03_B SES surface": minimum -29.31, mean -4.405, maximum 25.39 > interfaces sel & ~solvent 0 buried areas: > open 2pl6 Summary of feedback from opening 2pl6 fetched from pdb --- notes | Fetching compressed mmCIF 2pl6 from http://files.rcsb.org/download/2pl6.cif Fetching CCD HTG from http://ligand-expo.rcsb.org/reports/H/HTG/HTG.cif 2pl6 title: Monoclinic crystal structure of hydrophobin HFBII in presence of a detergent [more info...] Chain information for 2pl6 #4 --- Chain | Description A B C D E F G H | Hydrophobin-2 Non-standard residues in 2pl6 #4 --- HTG — heptyl 1-thiohexopyranoside 2pl6 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 5| author_defined_assembly 6| author_defined_assembly 7| author_defined_assembly 8| author_defined_assembly > hide #!3 models > ~select #3 2 models selected > select #4 4562 atoms, 4137 bonds, 1 model selected > view sel > hide sel atoms > hide sel cartoons > show sel surfaces > mlp sel Map values for surface "2pl6_A SES surface": minimum -24.08, mean -3.485, maximum 21.53 Map values for surface "2pl6_B SES surface": minimum -26.26, mean -3.658, maximum 20.56 Map values for surface "2pl6_C SES surface": minimum -27.11, mean -3.632, maximum 20.35 Map values for surface "2pl6_D SES surface": minimum -26.35, mean -3.657, maximum 22.81 Map values for surface "2pl6_E SES surface": minimum -26.07, mean -3.789, maximum 22.03 Map values for surface "2pl6_F SES surface": minimum -25.35, mean -3.704, maximum 19.34 Map values for surface "2pl6_G SES surface": minimum -26.94, mean -3.689, maximum 21.64 Map values for surface "2pl6_H SES surface": minimum -25.65, mean -3.519, maximum 22.02 > close #3 > close #4 > open2 > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/FEFEFKFK_model1.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/FEFEFKFK_model2.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/FEFEFKFK_model3.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/FEFEFKFK_model4.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/FEFEFKFK_model5.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/ST001_model1.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/ST001_model2.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/ST001_model3.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/ST001_model4.pdb > /Users/epkumpu/Documents/Projects/01_SEMMA/random_data/Predicted_peptide_structures/ST001_model5.pdb Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.056 -0.000 0.000 -0.083 -0.080 -6.428 -6.646 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.64637 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.149 -0.000 0.000 -0.088 -0.085 -6.256 -6.579 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.57877 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.058 -0.000 0.000 -0.083 -0.064 -6.284 -6.490 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.48961 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.052 -0.000 0.000 -0.083 -0.083 -6.249 -6.467 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.46668 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 8 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -0.082 -0.000 0.012 -0.083 0.021 -6.315 -6.447 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -6.44655 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 17 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -1.774 -0.754 0.368 -0.116 -0.027 -7.300 -9.603 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -9.60288 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 17 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -1.429 -0.985 0.206 -0.081 -0.111 -6.772 -9.170 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -9.17048 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 17 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -2.190 -0.447 0.326 0.065 0.046 -6.949 -9.148 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -9.14847 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 17 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -1.398 -1.042 0.410 -0.152 -0.019 -6.882 -9.084 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -9.08354 Ignored bad PDB record found on line 14 Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 8 REMARK Component boundaries: 0: 1 17 Ignored bad PDB record found on line 9 Ignored bad PDB record found on line 12 REMARK -2.460 -0.001 0.012 -0.247 -0.103 -6.265 -9.064 Ignored bad PDB record found on line 13 REMARK sOPEP Energy: -9.06411 Ignored bad PDB record found on line 14 FEFEFKFK_model1.pdb title: Protein t= 0.00000 [more info...] Chain information for FEFEFKFK_model1.pdb #3 --- Chain | Description | No description available FEFEFKFK_model2.pdb title: Protein t= 0.00000 [more info...] Chain information for FEFEFKFK_model2.pdb #4 --- Chain | Description | No description available FEFEFKFK_model3.pdb title: Protein t= 0.00000 [more info...] Chain information for FEFEFKFK_model3.pdb #5 --- Chain | Description | No description available FEFEFKFK_model4.pdb title: Protein t= 0.00000 [more info...] Chain information for FEFEFKFK_model4.pdb #6 --- Chain | Description | No description available FEFEFKFK_model5.pdb title: Protein t= 0.00000 [more info...] Chain information for FEFEFKFK_model5.pdb #7 --- Chain | Description | No description available ST001_model1.pdb title: Protein t= 0.00000 [more info...] Chain information for ST001_model1.pdb #8 --- Chain | Description | No description available ST001_model2.pdb title: Protein t= 0.00000 [more info...] Chain information for ST001_model2.pdb #9 --- Chain | Description | No description available ST001_model3.pdb title: Protein t= 0.00000 [more info...] Chain information for ST001_model3.pdb #10 --- Chain | Description | No description available ST001_model4.pdb title: Protein t= 0.00000 [more info...] Chain information for ST001_model4.pdb #11 --- Chain | Description | No description available ST001_model5.pdb title: Protein t= 0.00000 [more info...] Chain information for ST001_model5.pdb #12 --- Chain | Description | No description available > hide #8 models > hide #9 models > hide #11 models > hide #10 models > hide #12 models Unknown command: mmatch #4-7 to #3 > matchmaker #4-7 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FEFEFKFK_model1.pdb, chain (blank) (#3) with FEFEFKFK_model2.pdb, chain (blank) (#4), sequence alignment score = 40.4 RMSD between 5 pruned atom pairs is 0.866 angstroms; (across all 8 pairs: 4.104) Matchmaker FEFEFKFK_model1.pdb, chain (blank) (#3) with FEFEFKFK_model3.pdb, chain (blank) (#5), sequence alignment score = 40.4 RMSD between 8 pruned atom pairs is 1.170 angstroms; (across all 8 pairs: 1.170) Matchmaker FEFEFKFK_model1.pdb, chain (blank) (#3) with FEFEFKFK_model4.pdb, chain (blank) (#6), sequence alignment score = 40.4 RMSD between 8 pruned atom pairs is 0.581 angstroms; (across all 8 pairs: 0.581) Matchmaker FEFEFKFK_model1.pdb, chain (blank) (#3) with FEFEFKFK_model5.pdb, chain (blank) (#7), sequence alignment score = 40.4 RMSD between 8 pruned atom pairs is 0.789 angstroms; (across all 8 pairs: 0.789) Drag select of 405 atoms, 420 bonds > hide sel atoms > show sel cartoons > ui mousemode rightMode pivot > lighting full > view sel > ~select #3 324 atoms, 336 bonds, 4 models selected > ~select #4 243 atoms, 252 bonds, 3 models selected > ~select #5 162 atoms, 168 bonds, 2 models selected > ~select #6 81 atoms, 84 bonds, 1 model selected > ~select #7 Nothing selected > select #3 81 atoms, 84 bonds, 1 model selected > ~select #3 Nothing selected > hide #3-7 cartoons > show #3-7 surfaces > mlp #!3-7 Map values for surface "FEFEFKFK_model1.pdb_ SES surface": minimum -23.65, mean 0.2835, maximum 22.5 Map values for surface "FEFEFKFK_model2.pdb_ SES surface": minimum -21.25, mean -0.1356, maximum 22.36 Map values for surface "FEFEFKFK_model3.pdb_ SES surface": minimum -21.1, mean 0.4415, maximum 22.6 Map values for surface "FEFEFKFK_model4.pdb_ SES surface": minimum -24.01, mean 0.46, maximum 22.32 Map values for surface "FEFEFKFK_model5.pdb_ SES surface": minimum -20.35, mean 0.2021, maximum 23.54 > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > show #!6 models > hide #!5 models > hide #!6 models > show #!7 models > hide #!7 models > matchmaker #9-12 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ST001_model1.pdb, chain (blank) (#8) with ST001_model2.pdb, chain (blank) (#9), sequence alignment score = 77.9 RMSD between 10 pruned atom pairs is 0.484 angstroms; (across all 17 pairs: 4.517) Matchmaker ST001_model1.pdb, chain (blank) (#8) with ST001_model3.pdb, chain (blank) (#10), sequence alignment score = 86.9 RMSD between 6 pruned atom pairs is 0.964 angstroms; (across all 17 pairs: 5.859) Matchmaker ST001_model1.pdb, chain (blank) (#8) with ST001_model4.pdb, chain (blank) (#11), sequence alignment score = 86.9 RMSD between 8 pruned atom pairs is 1.418 angstroms; (across all 17 pairs: 3.804) Matchmaker ST001_model1.pdb, chain (blank) (#8) with ST001_model5.pdb, chain (blank) (#12), sequence alignment score = 86.9 RMSD between 7 pruned atom pairs is 1.433 angstroms; (across all 17 pairs: 6.738) > show #9 models > show #10 models > show #11 models > show #12 models > show #8 models > view > ui mousemode rightMode select > select #8:14 4 atoms, 3 bonds, 1 model selected > select clear > ui mousemode rightMode rotate > ui mousemode rightMode zoom > hide #8-12 surfaces > hide #8-12 cartoons > show #8-12 surfaces > mlp #!8-12 Map values for surface "ST001_model1.pdb_ SES surface": minimum -24.55, mean -3.803, maximum 19.36 Map values for surface "ST001_model2.pdb_ SES surface": minimum -26.62, mean -3.627, maximum 19.44 Map values for surface "ST001_model3.pdb_ SES surface": minimum -22.8, mean -4.155, maximum 19.62 Map values for surface "ST001_model4.pdb_ SES surface": minimum -26.48, mean -3.843, maximum 19.63 Map values for surface "ST001_model5.pdb_ SES surface": minimum -27.87, mean -3.208, maximum 18.74 > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > show #!11 models > hide #!10 models > hide #!11 models > show #!12 models > show #!11 models > show #!10 models > show #!9 models > show #!8 models > view > tile #8-12 columns 5 > save /Users/epkumpu/Desktop/image14.png supersample 3 > undo > turn y 90 > tile #8-12 columns 5 > save /Users/epkumpu/Desktop/image15.png supersample 3 > undo > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!3 models > view > tile #3-7 columns 5 > save /Users/epkumpu/Desktop/image16.png supersample 3 > undo > turn y 90 > tile #3-7 columns 5 > save /Users/epkumpu/Desktop/image17.png supersample 3 > undo > hide #!3-7 surfaces > show #!3-7 cartoons > hide #!3-7 surfaces > show #!3-7 surfaces > undo > tile #3-7 columns 5 > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > undo > undo > undo > undo > undo > undo > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > show #!11 models > show #!10 models > show #!9 models > show #!8 models > hide #!8-12 surfaces > show #!8-12 cartoons > view > hide #!8 models > show #!8 models > hide #!8 models > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!12 models > show #!12 models > show #!10 models > show #!8 models Drag select of 85 residues > show sel atoms > color sel byhetero > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > select clear > show #!8 surfaces > mlp #!8 Map values for surface "ST001_model1.pdb_ SES surface": minimum -24.55, mean -3.803, maximum 19.36 > select #8:9@O 1 atom, 1 model selected > select down 1 atom, 2 models selected > select up 12 atoms, 12 bonds, 2 models selected > select up 121 atoms, 123 bonds, 2 models selected > transparency sel 50 target s > select #8-12 605 atoms, 615 bonds, 5 models selected > transparency sel 50 target s > mlp sel Map values for surface "ST001_model1.pdb_ SES surface": minimum -24.55, mean -3.803, maximum 19.36 Map values for surface "ST001_model2.pdb_ SES surface": minimum -26.62, mean -3.627, maximum 19.44 Map values for surface "ST001_model3.pdb_ SES surface": minimum -22.8, mean -4.155, maximum 19.62 Map values for surface "ST001_model4.pdb_ SES surface": minimum -26.48, mean -3.843, maximum 19.63 Map values for surface "ST001_model5.pdb_ SES surface": minimum -27.87, mean -3.208, maximum 18.74 > select clear > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > show #!12 models > hide #!11 models > show #!11 models > hide #!12 models > color #!11 byhetero > color #!11 bychain > color #!11 byhetero > show #!10 models > hide #!10 models > select #8-12 605 atoms, 615 bonds, 5 models selected > color sel bychain > color sel byhetero > hide #!11 models > show #!8 models > select clear > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > show #!2 models > hide #!12 models > select #2:3@CE2 1 atom, 1 model selected > select up 12 atoms, 12 bonds, 2 models selected > select up 39 atoms, 39 bonds, 2 models selected > select up 63 atoms, 64 bonds, 2 models selected > transparency sel 50 target s > show sel atoms > color sel bychain > color sel byhetero > mlp sel Map values for surface "model1.pdb_ SES surface": minimum -23.48, mean -3.399, maximum 20.05 > hide #!2 models > ~select #2 1 model selected > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models Drag select of FEFEFKFK_model1.pdb_ SES surface, FEFEFKFK_model2.pdb_ SES surface, FEFEFKFK_model3.pdb_ SES surface, FEFEFKFK_model4.pdb_ SES surface, FEFEFKFK_model5.pdb_ SES surface, 40 residues > transparency sel 50 target s > show sel atoms > select clear > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!3 models > show #!4 models > show #!5 models > hide #!4 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!1 models > select #1 779 atoms, 733 bonds, 1 model selected > view sel > show sel surfaces > show sel cartoons > hide sel surfaces > color sel bychain > select clear > select #1/B:121 7 atoms, 7 bonds, 1 model selected > select up 47 atoms, 48 bonds, 2 models selected > select up 102 atoms, 94 bonds, 2 models selected Alignment identifier is 1.B > select clear > select #1/A:49 6 atoms, 5 bonds, 1 model selected > show sel atoms > select sel & @CA 2 atoms, 1 model selected > toolshed show Distances > distance #1/A:49@CA #1/B:120@CA Distance between 4mls.pdb #1/A SER 49 CA and /B LYS 120 CA: 30.535Å > open 6cvm 6cvm title: Atomic resolution cryo-EM structure of beta-galactosidase [more info...] Chain information for 6cvm #14 --- Chain | Description A B C D | Beta-galactosidase Non-standard residues in 6cvm #14 --- MG — magnesium ion NA — sodium ion PTQ — 2-phenylethyl 1-thio-beta-D-galactopyranoside (2-Phenylethyl beta-D- thiogalactoside, PETG) > select #14 37062 atoms, 33824 bonds, 76 pseudobonds, 2 models selected > ~select #14 Nothing selected > select #14 37062 atoms, 33824 bonds, 76 pseudobonds, 2 models selected > view sel > hide sel cartoons > select clear > hide #!1,14 cartoons > hide #!1,14 atoms > hide #!1,14 cartoons > select #14 37062 atoms, 33824 bonds, 76 pseudobonds, 2 models selected > show sel cartoons > color sel bychain > select #14/C:76 6 atoms, 5 bonds, 1 model selected > select up 43 atoms, 43 bonds, 1 model selected > select up 9267 atoms, 8456 bonds, 1 model selected > select up 37062 atoms, 33824 bonds, 1 model selected > select down 9267 atoms, 8456 bonds, 1 model selected Alignment identifier is 14.C > select #14 37062 atoms, 33824 bonds, 76 pseudobonds, 2 models selected > view sel > select clear > select clear > select #14/C:3 8 atoms, 7 bonds, 1 model selected > select #14/C:2 8 atoms, 7 bonds, 1 model selected > select sel & @CA 2 atoms, 1 model selected > distance #14/A:2@CA #14/C:2@CA Distance between 6cvm #14/A MET 2 CA and /C MET 2 CA: 130.091Å > select #14/D:433 8 atoms, 7 bonds, 1 model selected > select #14 37062 atoms, 33824 bonds, 77 pseudobonds, 3 models selected > ~select #14 Nothing selected > select #14 37062 atoms, 33824 bonds, 77 pseudobonds, 3 models selected > view sel > lighting full > lighting flat > select clear > set bgColor black > show #!1,14 surfaces > hide #1.2 models > hide #1.1 models > hide #!1 models > lighting full > hide #!14 surfaces > toolshed show "Cage Builder" > hide #!14 models > view sel > view sel Drag select of 85 atoms, 85 bonds > select clear > select up 2 atoms, 1 bond, 1 model selected > select up 110 atoms, 110 bonds, 1 model selected Drag select of 55 atoms, 55 bonds Drag select of 102 atoms, 102 bonds Drag select of 192 atoms, 196 bonds Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 47, in <lambda> b6.clicked.connect(lambda e: self.attach_polygons(6)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 47, in <lambda> b6.clicked.connect(lambda e: self.attach_polygons(6)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 47, in <lambda> b6.clicked.connect(lambda e: self.attach_polygons(6)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 47, in <lambda> b6.clicked.connect(lambda e: self.attach_polygons(6)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 44, in <lambda> b5.clicked.connect(lambda e: self.attach_polygons(5)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. Traceback (most recent call last): File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 47, in <lambda> b6.clicked.connect(lambda e: self.attach_polygons(6)) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/tool.py", line 81, in attach_polygons vertex_degree = d) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 44, in attach_polygons p = Polygon(session, n, radius, edge_thickness, edge_inset, color = color) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 120, in __init__ self._create_markers(session, color, markers, edges) File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) AttributeError: 'NoneType' object has no attribute 'create_marker' AttributeError: 'NoneType' object has no attribute 'create_marker' File "/Users/epkumpu/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cage_builder/cage.py", line 152, in _create_markers m = self.marker_set.create_marker(p, color, edge_radius) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.17 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Higher-Order Structure |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Adjusting cage-builder edge length: 'NoneType' object has no attribute 'create_marke |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed in tonight's ChimeraX build.
The problem was not with edge length. The error happened when creating a polygon with cage builder when other polygons had already been created but none of the existing polygons were selected to attach the new one. It was a typo in the code that it created a new cage but didn't assign the polygon.marker_set attribute to that new cage.